INTS11 p.Gln524=
c.1572G>A · VCV4821005
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.3%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.7 | GERP 0.93, phastCons 1 |
| Overall | ||
| CADD | 5.378 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.3%
African / African-American · 220/73,358 alleles
Filtering AF
0.267%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.255%
Overall
0.0159%
246/1,548,710 alleles · rare
exomes 108/1,397,028 · genomes 138/151,682 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.3% | 333 |
| Remaining individualsnot grpmax-eligible | 0.0217% | 4,614 |
| Admixed American | 0.0137% | 7,276 |
| South Asian | 0.00476% | 21,018 |
| European (non-Finnish) | 0.000174% | 573,243 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- INTS11
- Protein
- p.Gln524=
- Coding
- c.1572G>A
- MANE Select
- NM_017871
- Type
- single nucleotide variant
- Location
- chr1:1312261 (GRCh38)
- Gene constraint
- LOEUF 1.223 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.82 · 15 PDB
- Residue 524
- an α-helix
Similar variants
- INTS11 c.28+1406C>T Uncertain significance ★★ same type
- INTS11 p.Ala241Thr Uncertain significance ★★ ⚠ same type
- INTS11 p.Arg231Cys Uncertain significance ★★ ⚠ same type
- INTS11 p.Gln467His Uncertain significance ★★ ⚠ same type
- INTS11 p.Glu227Lys Uncertain significance ★★ same type
- INTS11 p.His157Arg Uncertain significance ★★ ⚠ same type
- INTS11 c.1607+18C>A Benign ★★ same type
- INTS11 p.Arg196= Benign ★★ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/ints11-p-gln524 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown